We have developed cap analysis of gene expression (CAGE) to simultaneously map mRNAs and long non-coding RNAs (lncRNAs) transcription starting sites (TSSs) and measure their expression at each different promoters. Since CAGE shows single nucleotide resolution, we can use this technology to comprehensively measure gene expression at each TSSs. Due to this unprecedented resolution, we have learned that promoters use different regulatory elements in different cells and tissues. Using CAGE, we can also infer the transcriptional networks that regulate gene expression in each different cell type. For its high resolution to map TSSs, CAGE has also been used extensively in the ENCODE (1) and modENCODE (2) projects.
In the Functional Annotation of the Mammalian Genome (FANTOM) 5 project, we have applied CAGE on a comprehensive panel of human and mouse primary cells and other tissues, resulting in a very broad map of the promoterome and regulatory networks (3). Our map revealed the existence of 201,802 and 158,966 promoters and 65,423 and 44,459 enhancers, in human and mouse respectively, which are often tissue specific. The project also revealed complexity of genome activation hierarchy in which transcription initiates with enhancers followed by promoters and then other genes in high density of time course expression analysis profiling 33 mouse/human biological systems (4). The FANTOM5 database is one of the broadest expression database available to the community (http://fantom.gsc.riken.jp/5/). Additionally, we have focused on nuclear RNAs and determined the pattern of expression of retrotransposon elements (RE), which are likely to have a regulatory role. As example, some families of LTR retrotransposon elements are specifically expressed in ES and iPS cells, where they have a role in maintenance of pluripotency (5). In general, CAGE analysis of nuclear RNA is a very powerful tool to interrogate nuclear RNAs expression as a proxy for epigenome activity.
Ongoing FANTOM6 project is focusing on broad understanding for the function and the interaction with cell regulatory networks of these RNAs in several primary cells, with the purpose to create the broadest database of functional lncRNAs.
1. ENCODE Project Consortium, Nature 489, 57-74 (2012)
2. Chen et al., Genome Research 24, 1209-1223 (2014)
3. Forrest et al., Nature 507, 462-470 (2014)
4. Arner et al., Science 347, 1010-1014 (2015)
5. Fort et al., Nature Genetics 46, 558-566 (2014)